717 research outputs found
A History of Hyperactive Chemistry on the Web: From Text and Images to Objects, Models, and Molecular Components
The chemical application of the Internet over the last decade is reviewed, and lessons from the experience set out. In particular, we emphasize that to create a high quality, indexed and structured chemical resource using this technology, new standards and methodologies have to be defined
and adopted. One particular change, from the traditional use of text and illustrations in printed journals, to the deployment of object-based models built from, e.g., molecular components is discussed in more detail
Hearings: Pell Statements (1976): Report 02
Archive of work produced using the resources of the Imperial College High Performance Computing Service
Communication and re-use of chemical information in bioscience.
The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.An article submitted to BiomedCentral Bioinformatics, created on request with their Publicon system. The transformed manuscript is archived as PDF. Although it has been through the publishers system this is purely automatic and the contents are those of a pre-refereed preprint. The formatting is provided by the system and tables and figures appear at the end. An accommpanying submission, http://www.dspace.cam.ac.uk/handle/1810/34580, describes the rationale and cultural aspects of publishing , abstracting and aggregating chemical information. BMC is an Open Access publisher and we emphasize that all content is re-usable under Creative Commons Licens
Chemistry in Bioinformatics
A preprint of an invited submission to BioMedCentral Bioinformatics. This short manuscript is an overview or the current problems and opportunities in publishing chemical information. Full details of technology are given in the sibling manuscript http://www.dspace.cam.ac.uk/handle/1810/34579
The manuscript is the authors' preprint although it has been automatically transformed into this archived PDF by the submission system. The authors are not responsible for the formattingChemical information is now seen as critical for most areas
of life sciences. But unlike Bioinformatics, where data is
Openly available and freely re−usable, most chemical
information is closed and cannot be re−distributed without
permission. This has led to a failure to adopt modern
informatics and software techniques and therefore paucity of
chemistry in bioinformatics. New technology, however, offers
the hope of making chemical data (compounds and properties)
Free during the authoring process. We argue that the technology
is already available; we require a collective agreement to
enhance publication protocols
Semantic physical science.
The articles in this special issue arise from a workshop and symposium held in January 2012 (Semantic Physical Science'). We invited people who shared our vision for the potential of the web to support chemical and related subjects. Other than the initial invitations, we have not exercised any control over the content of the contributed articles.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are
The vicinal difluoro motif : the synthesis and conformation of erythro- and threo-diastereoisomers of 1,2-difluorodiphenylethanes, 2,3-difluorosuccinic acids and their derivatives
Background: It is well established that vicinal fluorines (RCHF-CHFR) prefer to adopt a gauche rather than an anti conformation when placed along aliphatic chains. This has been particularly recognised for 1,2-difluoroethane and extends to 2,3-difluorobutane and longer alkyl chains. It follows in these latter cases that if erythro and threo vicinal difluorinated stereoisomers are compared, they will adopt different overall conformations if the fluorines prefer to be gauche in each case. This concept is explored in this paper with erythro- and threo- diastereoisomers of 2,3-difluorosuccinates. Results: A synthetic route to 2,3-difluorosuccinates has been developed through erythro- and threo- 1,2-difluoro-1,2-diphenylethane which involved the oxidation of the aryl rings to generate the corresponding 2,3- difluorosuccinic acids. Ester and amide derivatives of the erythro- and threo- 2,3-difluorosuccinic acids were then prepared. The solid and solution state conformation of these compounds was assessed by X-ray crystallography and NMR. Ab initio calculations were also carried out to model the conformation of erythro- and threo- 1,2-difluoro-1,2-diphenylethane as these differed from the 2,3-difluorosuccinates. Conclusion: In general the overall chain conformations of the 2,3-difluorosuccinates diastereoisomers were found to be influenced by the fluorine gauche effect. The study highlights the prospects of utilising the vicinal difluorine motif (RCHF-CHFR) as a tool for influencing the conformation of performance organic molecules and particularly tuning conformation by selecting specific diastereoisomers (erythro or threo).Publisher PDFPeer reviewe
Chemistry in bioinformatics.
Chemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols.Rights : This article is licensed under the BioMed Central license at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution License'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are
A data-oriented approach to making new molecules as a student experiment: AI-enabling FAIR publication of NMR data for organic esters
open access articleThe lack of machine-readable data is a major obstacle in the application of NMR in artificial intelligence. As a way to overcome this, a procedure for capturing primary NMR Spectroscopic instrumental data annotated with rich metadata and publication in a FAIR data repository is described as part of an undergraduate student laboratory experiment in a chemistry department. This couples the techniques of chemical synthesis of a never before made organic ester with illustration of modern data management practices and serves to raise student awareness of how FAIR data might improve research quality and replicability. Searches of the registered metadata are shown which enable actionable Finding and Accessing of such data. The potential for Re-use of the data in AI-applications is discussed
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Extracting and re-using research data from chemistry e-theses: the SPECTRa-T project
Scientific e-theses are data-rich resources, but much of the information they contain is not readily accessible. For chemistry, the SPECTRa-T project has addressed this problem by developing data-mining techniques to extract experimental data, creating RDF (Resource Description Framework) triples for exposure to sophisticated Semantic Web searches.
We used OSCAR3, an Open Source chemistry text-mining tool, to parse and extract data from theses in PDF, and from theses in Office Open XML document format.
Theses in PDF suffered data corruption and a loss of formatting that prevented the identification of chemical objects. Theses in .docx yielded semantically rich SciXML that enabled the additional extraction of associated data. Chemical objects were placed in a data repository, and RDF triples deposited in a triplestore.
Data-mining from chemistry e-theses is both desirable and feasible; but the use of PDF, the de facto format standard for deposit in most repositories, prevents the optimal extraction of data for semantic querying. In order to facilitate this, we recommend that universities also require deposition of chemistry e-theses in an XML document format. Further work is required to clarify the complex IPR issues and ensure that they do not become an unwarranted barrier to data extraction and re-use
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